[Bioperl-l] Deobfuscator interface now available

[Chris Fields]

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Sendu Bala
> Sent: Monday, May 15, 2006 8:09 AM
> To: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Deobfuscator interface now available
> 
> Amir Karger wrote:
> > This tool is quite nice, and may save me a lot of perdoc'ing.
> 
> Yes, many thanks to everyone involved.

The Deobfuscator currently indexes bioperl-1.4, so it's not completely
up-to-date.  I believe Mauricio and Dave may be working on updating to the
newer versions and maybe bioperl-live, as well as getting the other bioperl
packages up and running.

For modules added after v1.4 I use the script in the FAQ question mentioned
on the Deobfuscator wiki page to get up-to-date methods, then grab the that
ActiveState HTML'd perldocs pumped out when installing using PPM (I make a
custom PPM/PPD file and install myself every once in a while):

#!/usr/bin/perl -w
use Class::Inspector;
$class = shift || die "Usage: methods perl_class_name\n";
eval "require $class";
print join ("\n", sort @{Class::Inspector-

> > A couple of minor interface thoughts.
> >
> > 1)There's quite a lot of methods for many of the classes. As such, I
> > think I'll often want to browse through what's available in a class. But
> > 60% or so of the screen real estate is used for "Enter a search
> > string... OR select a class from the list". IMO, it would be better to
> > have two pages, a search page and a result page.   It only takes a click
> > on Back (or a "new search" button) to get to a new search, and now you
> > can use your whole screen for reading your results.
> 
> As the compromise it must be, I like the way it behaves. I don't like
> lots of windows. I especially don't like pop up windows. Right now when
> I'm using the bioperl docs I tend to have a whole bunch of tabs open to
> different class pages at once, so being able to see an overview all on
> one page in Deobfuscator is very nice.
>
> Further to that, I'd love it if clicking on a method name caused an
> in-place css(&|javascript) reveal (similar to how a well implemented
> drop down menu works in a website) rather than a new window opened.
> Alternatively, just have more columns in the results table, ie. usage,
> function, returns, args columns. I feel that opening a window for each
> method you want to understand is far too slow.

Agreed.

> I'd also really like a link to the code for the method as well. The
> bioperl docs are rarely complete enough that you can really understand
> what every method is supposed to do without looking at the code.

The methods that pop up are in columns along with the class module that
implements the method.  


If you click on that link you get PDOC documentation for the module which
includes most of the code (strangely, though Deobfuscator indexes bioperl
1.4, the PDOC corresponds to bioperl-live).  Is that what you meant, or
something a bit more detailed?

> > 3) Minimalist is nice, but documentation is even nicer. It wasn't clear
> > to me that the search searches within class names rather than function
> > names. What I really want to know sometimes is which module has, say,
> > the revcom method in it.

That's listed in the method results table (the next column has the module
with a link to the module's online docs).


Chris


> This would be a great feature to add.
> 
> 
> Another minor interface thought:
> 6) Have a little more cell padding in all the tables. Things are just a
> little too cramped and things start to look messy/ run into each other.
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